Sliding Windows Analysis

Alewife Populations of Interest Subset

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mxn10_plot <- ggplot(data = mxn10, 
                     mapping = aes(x = pos_cum, 
                                   y = Fst, 
                                   color = as_factor(chr))) +
  geom_point(alpha = 0.75, size = 0.5) +
  scale_x_continuous(label = mxn10_axis_set$chr, 
                     breaks = mxn10_axis_set$center) +
  scale_y_continuous(expand = c(0,0), 
                     limits = c(-0.05, 1)) +
  scale_color_manual(values = rep(c("#242b35", "#869ca8"), 
                                  unique(length(mxn10_axis_set$chr)))) +
  labs(x = NULL, 
       y = "Fst", 
       title = "Mid-Atlantic vs N. Atlantic Anadromous Alewife", 
       subtitle = "Size 10,000 Step 2,000") +
  theme_bw() +
  theme(legend.position = "none",
        panel.grid.major.x = element_blank(),
        panel.grid.minor.x = element_blank(),
        axis.title.y = element_markdown(),
        axis.text.x = element_text(angle = 90,
                                  size = 8,
                                  vjust = 0.5))
mxn10_plot

mxn50_plot <- ggplot(data = mxn50, 
                     mapping = aes(x = pos_cum, 
                                   y = Fst, 
                                   color = as_factor(chr))) +
  geom_point(alpha = 0.75, size = 0.5) +
  scale_x_continuous(label = mxn50_axis_set$chr, 
                     breaks = mxn50_axis_set$center) +
  scale_y_continuous(expand = c(0,0), 
                     limits = c(-0.05, 1)) +
  scale_color_manual(values = rep(c("#242b35", "#869ca8"), 
                                  unique(length(mxn50_axis_set$chr)))) +
  labs(x = NULL, 
       y = "Fst", 
       title = "Mid-Atlantic vs N. Atlantic Anadromous Alewife", 
       subtitle = "Size 50,000 Step 10,000") +
  theme_bw() +
  theme(legend.position = "none",
        panel.grid.major.x = element_blank(),
        panel.grid.minor.x = element_blank(),
        axis.title.y = element_markdown(),
        axis.text.x = element_text(angle = 90,
                                  size = 8,
                                  vjust = 0.5))
mxn50_plot

### Regions of Interest ###
## Looking at Chromosomes with Fst of 0.25 or greater ##
mxn50_chr1_plot <- ggplot(data = filter(mxn50, chr == "NC_055957.1"), 
                          mapping = aes(x = pos_cum, 
                                        y = Fst)) +
  geom_point(alpha = 0.75, size = 0.5, color = "#242b35") +
  scale_x_continuous(label = mxn50_axis_set$chr, 
                     breaks = mxn50_axis_set$center) +
  scale_y_continuous(expand = c(0,0), 
                     limits = c(-0.05, 1)) +
  labs(x = NULL, 
       y = "Fst", 
       title = "Mid-Atlantic vs N. Atlantic Anadromous Alewife", 
       subtitle = "Size 50,000 Step 10,000") +
  theme_bw() +
  theme(legend.position = "none",
        panel.grid.major.x = element_blank(),
        panel.grid.minor.x = element_blank(),
        axis.title.y = element_markdown(),
        axis.text.x = element_text(angle = 90,
                                  size = 8,
                                  vjust = 0.5))
mxn50_chr1_plot

mxn50_chr2_plot <- ggplot(data = filter(mxn50, chr == "NC_055958.1"), 
                          mapping = aes(x = pos_cum, 
                                        y = Fst)) +
  geom_point(alpha = 0.75, size = 0.5, color = "#869ca8") +
  scale_x_continuous(label = mxn50_axis_set$chr, 
                     breaks = mxn50_axis_set$center) +
  scale_y_continuous(expand = c(0,0), 
                     limits = c(-0.05, 1)) +
  labs(x = NULL, 
       y = "Fst", 
       title = "Mid-Atlantic vs N. Atlantic Anadromous Alewife", 
       subtitle = "Size 50,000 Step 10,000") +
  theme_bw() +
  theme(legend.position = "none",
        panel.grid.major.x = element_blank(),
        panel.grid.minor.x = element_blank(),
        axis.title.y = element_markdown(),
        axis.text.x = element_text(angle = 90,
                                  size = 8,
                                  vjust = 0.5))
mxn50_chr2_plot

mxn50_chr3_plot <- ggplot(data = filter(mxn50, chr == "NC_055959.1"), 
                          mapping = aes(x = pos_cum, 
                                        y = Fst)) +
  geom_point(alpha = 0.75, size = 0.5, color = "#869ca8") +
  scale_x_continuous(label = mxn50_axis_set$chr, 
                     breaks = mxn50_axis_set$center) +
  scale_y_continuous(expand = c(0,0), 
                     limits = c(-0.05, 1)) +
  labs(x = NULL, 
       y = "Fst", 
       title = "Mid-Atlantic vs N. Atlantic Anadromous Alewife", 
       subtitle = "Size 50,000 Step 10,000") +
  theme_bw() +
  theme(legend.position = "none",
        panel.grid.major.x = element_blank(),
        panel.grid.minor.x = element_blank(),
        axis.title.y = element_markdown(),
        axis.text.x = element_text(angle = 90,
                                  size = 8,
                                  vjust = 0.5))
mxn50_chr3_plot

mxn50_chr10_plot <- ggplot(data = filter(mxn50, chr == "NC_055966.1"), 
                           mapping = aes(x = pos_cum, 
                                         y = Fst)) +
  geom_point(alpha = 0.75, size = 0.5, color = "#242b35") +
  scale_x_continuous(label = mxn50_axis_set$chr, 
                     breaks = mxn50_axis_set$center) +
  scale_y_continuous(expand = c(0,0), 
                     limits = c(-0.05, 1)) +
  labs(x = NULL, 
       y = "Fst", 
       title = "Mid-Atlantic vs N. Atlantic Anadromous Alewife", 
       subtitle = "Size 50,000 Step 10,000") +
  theme_bw() +
  theme(legend.position = "none",
        panel.grid.major.x = element_blank(),
        panel.grid.minor.x = element_blank(),
        axis.title.y = element_markdown(),
        axis.text.x = element_text(angle = 90,
                                  size = 8,
                                  vjust = 0.5))
mxn50_chr10_plot

mxn50_chr12_plot <- ggplot(data = filter(mxn50, chr == "NC_055968.1"), 
                           mapping = aes(x = pos_cum, 
                                          y = Fst)) +
  geom_point(alpha = 0.75, size = 0.5, color = "#242b35") +
  scale_x_continuous(label = mxn50_axis_set$chr, 
                     breaks = mxn50_axis_set$center) +
  scale_y_continuous(expand = c(0,0), 
                     limits = c(-0.05, 1)) +
  labs(x = NULL, 
       y = "Fst", 
       title = "Mid-Atlantic vs N. Atlantic Anadromous Alewife", 
       subtitle = "Size 50,000 Step 10,000") +
  theme_bw() +
  theme(legend.position = "none",
        panel.grid.major.x = element_blank(),
        panel.grid.minor.x = element_blank(),
        axis.title.y = element_markdown(),
        axis.text.x = element_text(angle = 90,
                                  size = 8,
                                  vjust = 0.5))
mxn50_chr12_plot

### Chromosome 2 Spike Region ###

mxn50_spike_plot <- mxn50 %>%
  filter(chr == "NC_055958.1") %>%
  filter(midPos >= 16600000) %>%
  filter(midPos <= 17000000) %>%
  ggplot(.,
         mapping = aes(x = midPos, 
                       y = Fst, 
                       size = Nsites)) +
  geom_point(alpha = 0.75, color = "#869ca8") +
  scale_y_continuous(expand = c(0,0), 
                     limits = c(-0.05, 1)) +
  scale_size_continuous(range = c(0.5, 3)) +
  labs(x = "Position", 
       y = "Fst", 
       title = "Mid-Atlantic vs N. Atlantic Anadromous Alewife Chromosome 2", 
       subtitle = "Size 50,000 Step 10,000") +
  theme_bw() +
  theme(legend.position = "none",
        panel.grid.major.x = element_blank(),
        panel.grid.minor.x = element_blank(),
        axis.title.y = element_markdown(),
        axis.text.x = element_text(angle = 90,
                                  size = 8,
                                  vjust = 0.5))
mxn50_spike_plot

mxg10_plot <- ggplot(data = mxg10, 
                     mapping = aes(x = pos_cum, 
                                   y = Fst, 
                                   color = as_factor(chr))) +
  geom_point(alpha = 0.75, size = 0.5) +
  scale_x_continuous(label = mxg10_axis_set$chr, 
                     breaks = mxg10_axis_set$center) +
  scale_y_continuous(expand = c(0,0), 
                     limits = c(-0.05, 1)) +
  scale_color_manual(values = rep(c("#242b35", "#869ca8"), 
                                  unique(length(mxg10_axis_set$chr)))) +
  labs(x = NULL, 
       y = "Fst", 
       title = "Mid-Atlantic Anadromous vs Great Lakes Landlocked Alewife", 
       subtitle = "Size 10,000 Step 2,000") +
  theme_bw() +
  theme(legend.position = "none",
        panel.grid.major.x = element_blank(),
        panel.grid.minor.x = element_blank(),
        axis.title.y = element_markdown(),
        axis.text.x = element_text(angle = 90,
                                  size = 8,
                                  vjust = 0.5))
mxg10_plot

mxg50_plot <- ggplot(data = mxg50, 
                     mapping = aes(x = pos_cum, 
                                   y = Fst, 
                                   color = as_factor(chr))) +
  geom_point(alpha = 0.75, size = 0.5) +
  scale_x_continuous(label = mxg50_axis_set$chr, 
                     breaks = mxg50_axis_set$center) +
  scale_y_continuous(expand = c(0,0), 
                     limits = c(-0.05, 1)) +
  scale_color_manual(values = rep(c("#242b35", "#869ca8"), 
                                  unique(length(mxg50_axis_set$chr)))) +
  labs(x = NULL, 
       y = "Fst", 
       title = "Mid-Atlantic Anadromous vs Great Lakes Landlocked Alewife", 
       subtitle = "Size 50,000 Step 10,000") +
  theme_bw() +
  theme(legend.position = "none",
        panel.grid.major.x = element_blank(),
        panel.grid.minor.x = element_blank(),
        axis.title.y = element_markdown(),
        axis.text.x = element_text(angle = 90,
                                  size = 8,
                                  vjust = 0.5))
mxg50_plot

### Regions of Interest ###
## Looking at the same chromosomes for MIDA vs NATLA ##
mxg50_chr1_plot <- ggplot(data = filter(mxg50, chr == "NC_055957.1"), 
                     mapping = aes(x = pos_cum, 
                                   y = Fst)) +
  geom_point(alpha = 0.75, size = 0.5, color = "#242b35") +
  scale_x_continuous(label = mxg50_axis_set$chr, 
                     breaks = mxg50_axis_set$center) +
  scale_y_continuous(expand = c(0,0), 
                     limits = c(-0.05, 1)) +
  labs(x = NULL, 
       y = "Fst", 
       title = "Mid-Atlantic Anadromous vs Great Lakes Landlocked Alewife", 
       subtitle = "Size 50,000 Step 10,000") +
  theme_bw() +
  theme(legend.position = "none",
        panel.grid.major.x = element_blank(),
        panel.grid.minor.x = element_blank(),
        axis.title.y = element_markdown(),
        axis.text.x = element_text(angle = 90,
                                  size = 8,
                                  vjust = 0.5))
mxg50_chr1_plot

mxg50_chr2_plot <- ggplot(data = filter(mxg50, chr == "NC_055958.1"), 
                     mapping = aes(x = pos_cum, 
                                   y = Fst)) +
  geom_point(alpha = 0.75, size = 0.5, color = "#869ca8") +
  scale_x_continuous(label = mxg50_axis_set$chr, 
                     breaks = mxg50_axis_set$center) +
  scale_y_continuous(expand = c(0,0), 
                     limits = c(-0.05, 1)) +
  labs(x = NULL, 
       y = "Fst", 
       title = "Mid-Atlantic Anadromous vs Great Lakes Landlocked Alewife", 
       subtitle = "Size 50,000 Step 10,000") +
  theme_bw() +
  theme(legend.position = "none",
        panel.grid.major.x = element_blank(),
        panel.grid.minor.x = element_blank(),
        axis.title.y = element_markdown(),
        axis.text.x = element_text(angle = 90,
                                  size = 8,
                                  vjust = 0.5))
mxg50_chr2_plot

mxg50_chr3_plot <- ggplot(data = filter(mxg50, chr == "NC_055959.1"), 
                     mapping = aes(x = pos_cum, 
                                   y = Fst)) +
  geom_point(alpha = 0.75, size = 0.5, color = "#869ca8") +
  scale_x_continuous(label = mxg50_axis_set$chr, 
                     breaks = mxg50_axis_set$center) +
  scale_y_continuous(expand = c(0,0), 
                     limits = c(-0.05, 1)) +
  labs(x = NULL, 
       y = "Fst", 
       title = "Mid-Atlantic Anadromous vs Great Lakes Landlocked Alewife", 
       subtitle = "Size 50,000 Step 10,000") +
  theme_bw() +
  theme(legend.position = "none",
        panel.grid.major.x = element_blank(),
        panel.grid.minor.x = element_blank(),
        axis.title.y = element_markdown(),
        axis.text.x = element_text(angle = 90,
                                  size = 8,
                                  vjust = 0.5))
mxg50_chr3_plot

mxg50_chr10_plot <- ggplot(data = filter(mxg50, chr == "NC_055966.1"), 
                     mapping = aes(x = pos_cum, 
                                   y = Fst)) +
  geom_point(alpha = 0.75, size = 0.5, color = "#242b35") +
  scale_x_continuous(label = mxg50_axis_set$chr, 
                     breaks = mxg50_axis_set$center) +
  scale_y_continuous(expand = c(0,0), 
                     limits = c(-0.05, 1)) +
  labs(x = NULL, 
       y = "Fst", 
       title = "Mid-Atlantic Anadromous vs Great Lakes Landlocked Alewife", 
       subtitle = "Size 50,000 Step 10,000") +
  theme_bw() +
  theme(legend.position = "none",
        panel.grid.major.x = element_blank(),
        panel.grid.minor.x = element_blank(),
        axis.title.y = element_markdown(),
        axis.text.x = element_text(angle = 90,
                                  size = 8,
                                  vjust = 0.5))
mxg50_chr10_plot

mxg50_chr12_plot <- ggplot(data = filter(mxg50, chr == "NC_055968.1"), 
                     mapping = aes(x = pos_cum, 
                                   y = Fst)) +
  geom_point(alpha = 0.75, size = 0.5, color = "#242b35") +
  scale_x_continuous(label = mxg50_axis_set$chr, 
                     breaks = mxg50_axis_set$center) +
  scale_y_continuous(expand = c(0,0), 
                     limits = c(-0.05, 1)) +
  labs(x = NULL, 
       y = "Fst", 
       title = "Mid-Atlantic Anadromous vs Great Lakes Landlocked Alewife", 
       subtitle = "Size 50,000 Step 10,000") +
  theme_bw() +
  theme(legend.position = "none",
        panel.grid.major.x = element_blank(),
        panel.grid.minor.x = element_blank(),
        axis.title.y = element_markdown(),
        axis.text.x = element_text(angle = 90,
                                  size = 8,
                                  vjust = 0.5))
mxg50_chr12_plot

### Chromosome 2 Spike Region ###

mxg50_spike_plot <- mxg50 %>%
  filter(chr == "NC_055958.1") %>%
  filter(midPos >= 16600000) %>%
  filter(midPos <= 17000000) %>%
  ggplot(.,
         mapping = aes(x = midPos, 
                       y = Fst, 
                       size = Nsites)) +
  geom_point(alpha = 0.75, color = "#869ca8") +
  scale_y_continuous(expand = c(0,0), 
                     limits = c(-0.05, 1)) +
  scale_size_continuous(range = c(0.5, 3)) +
  labs(x = "Position", 
       y = "Fst", 
       title = "Mid-Atlantic Anadromous vs Great Lakes Landlocked Alewife Chromosome 2", 
       subtitle = "Size 50,000 Step 10,000") +
  theme_bw() +
  theme(legend.position = "none",
        panel.grid.major.x = element_blank(),
        panel.grid.minor.x = element_blank(),
        axis.title.y = element_markdown(),
        axis.text.x = element_text(angle = 90,
                                  size = 8,
                                  vjust = 0.5))
mxg50_spike_plot

nxg10_plot <- ggplot(data = nxg10, 
                     mapping = aes(x = pos_cum, 
                                   y = Fst, 
                                   color = as_factor(chr))) +
  geom_point(alpha = 0.75, size = 0.5) +
  scale_x_continuous(label = nxg10_axis_set$chr, 
                     breaks = nxg10_axis_set$center) +
  scale_y_continuous(expand = c(0,0), 
                     limits = c(-0.05, 1)) +
  scale_color_manual(values = rep(c("#242b35", "#869ca8"), 
                                  unique(length(nxg10_axis_set$chr)))) +
  labs(x = NULL, 
       y = "Fst", 
       title = "N. Atlantic Anadromous vs Great Lakes Landlocked Alewife", 
       subtitle = "Size 10,000 Step 2,000") +
  theme_bw() +
  theme(legend.position = "none",
        panel.grid.major.x = element_blank(),
        panel.grid.minor.x = element_blank(),
        axis.title.y = element_markdown(),
        axis.text.x = element_text(angle = 90,
                                  size = 8,
                                  vjust = 0.5))
nxg10_plot

nxg50_plot <- ggplot(data = nxg50, 
                     mapping = aes(x = pos_cum, 
                                   y = Fst, 
                                   color = as_factor(chr))) +
  geom_point(alpha = 0.75, size = 0.5) +
  scale_x_continuous(label = nxg50_axis_set$chr, 
                     breaks = nxg50_axis_set$center) +
  scale_y_continuous(expand = c(0,0), 
                     limits = c(-0.05, 1)) +
  scale_color_manual(values = rep(c("#242b35", "#869ca8"), 
                                  unique(length(nxg50_axis_set$chr)))) +
  labs(x = NULL, 
       y = "Fst", 
       title = "N. Atlantic Anadromous vs Great Lakes Landlocked Alewife", 
       subtitle = "Size 50,000 Step 10,000") +
  theme_bw() +
  theme(legend.position = "none",
        panel.grid.major.x = element_blank(),
        panel.grid.minor.x = element_blank(),
        axis.title.y = element_markdown(),
        axis.text.x = element_text(angle = 90,
                                  size = 8,
                                  vjust = 0.5))
nxg50_plot

### Regions of Interest ###
## Looking at the same chromosomes for MIDA vs NATLA ##
nxg50_chr1_plot <- ggplot(data = filter(nxg50, chr == "NC_055957.1"), 
                     mapping = aes(x = pos_cum, 
                                   y = Fst)) +
  geom_point(alpha = 0.75, size = 0.5, color = "#242b35") +
  scale_x_continuous(label = nxg50_axis_set$chr, 
                     breaks = nxg50_axis_set$center) +
  scale_y_continuous(expand = c(0,0), 
                     limits = c(-0.05, 1)) +
  labs(x = NULL, 
       y = "Fst", 
       title = "N. Atlantic Anadromous vs Great Lakes Landlocked Alewife", 
       subtitle = "Size 50,000 Step 10,000") +
  theme_bw() +
  theme(legend.position = "none",
        panel.grid.major.x = element_blank(),
        panel.grid.minor.x = element_blank(),
        axis.title.y = element_markdown(),
        axis.text.x = element_text(angle = 90,
                                  size = 8,
                                  vjust = 0.5))
nxg50_chr1_plot

nxg50_chr2_plot <- ggplot(data = filter(nxg50, chr == "NC_055958.1"), 
                     mapping = aes(x = pos_cum, 
                                   y = Fst)) +
  geom_point(alpha = 0.75, size = 0.5, color = "#869ca8") +
  scale_x_continuous(label = nxg50_axis_set$chr, 
                     breaks = nxg50_axis_set$center) +
  scale_y_continuous(expand = c(0,0), 
                     limits = c(-0.05, 1)) +
  labs(x = NULL, 
       y = "Fst", 
       title = "N. Atlantic Anadromous vs Great Lakes Landlocked Alewife", 
       subtitle = "Size 50,000 Step 10,000") +
  theme_bw() +
  theme(legend.position = "none",
        panel.grid.major.x = element_blank(),
        panel.grid.minor.x = element_blank(),
        axis.title.y = element_markdown(),
        axis.text.x = element_text(angle = 90,
                                  size = 8,
                                  vjust = 0.5))
nxg50_chr2_plot

nxg50_chr3_plot <- ggplot(data = filter(nxg50, chr == "NC_055959.1"), 
                     mapping = aes(x = pos_cum, 
                                   y = Fst)) +
  geom_point(alpha = 0.75, size = 0.5, color = "#869ca8") +
  scale_x_continuous(label = nxg50_axis_set$chr, 
                     breaks = nxg50_axis_set$center) +
  scale_y_continuous(expand = c(0,0), 
                     limits = c(-0.05, 1)) +
  labs(x = NULL, 
       y = "Fst", 
       title = "N. Atlantic Anadromous vs Great Lakes Landlocked Alewife", 
       subtitle = "Size 50,000 Step 10,000") +
  theme_bw() +
  theme(legend.position = "none",
        panel.grid.major.x = element_blank(),
        panel.grid.minor.x = element_blank(),
        axis.title.y = element_markdown(),
        axis.text.x = element_text(angle = 90,
                                  size = 8,
                                  vjust = 0.5))
nxg50_chr3_plot

nxg50_chr10_plot <- ggplot(data = filter(nxg50, chr == "NC_055966.1"), 
                     mapping = aes(x = pos_cum, 
                                   y = Fst)) +
  geom_point(alpha = 0.75, size = 0.5, color = "#242b35") +
  scale_x_continuous(label = nxg50_axis_set$chr, 
                     breaks = nxg50_axis_set$center) +
  scale_y_continuous(expand = c(0,0), 
                     limits = c(-0.05, 1)) +
  labs(x = NULL, 
       y = "Fst", 
       title = "N. Atlantic Anadromous vs Great Lakes Landlocked Alewife", 
       subtitle = "Size 50,000 Step 10,000") +
  theme_bw() +
  theme(legend.position = "none",
        panel.grid.major.x = element_blank(),
        panel.grid.minor.x = element_blank(),
        axis.title.y = element_markdown(),
        axis.text.x = element_text(angle = 90,
                                  size = 8,
                                  vjust = 0.5))
nxg50_chr10_plot

nxg50_chr12_plot <- ggplot(data = filter(nxg50, chr == "NC_055968.1"), 
                     mapping = aes(x = pos_cum, 
                                   y = Fst)) +
  geom_point(alpha = 0.75, size = 0.5, color = "#242b35") +
  scale_x_continuous(label = nxg50_axis_set$chr, 
                     breaks = nxg50_axis_set$center) +
  scale_y_continuous(expand = c(0,0), 
                     limits = c(-0.05, 1)) +
  labs(x = NULL, 
       y = "Fst", 
       title = "N. Atlantic Anadromous vs Great Lakes Landlocked Alewife", 
       subtitle = "Size 50,000 Step 10,000") +
  theme_bw() +
  theme(legend.position = "none",
        panel.grid.major.x = element_blank(),
        panel.grid.minor.x = element_blank(),
        axis.title.y = element_markdown(),
        axis.text.x = element_text(angle = 90,
                                  size = 8,
                                  vjust = 0.5))
nxg50_chr12_plot

### Chromosome 2 Spike Region ###

nxg50_spike_plot <- nxg50 %>%
  filter(chr == "NC_055958.1") %>%
  filter(midPos >= 16600000) %>%
  filter(midPos <= 17000000) %>%
  ggplot(.,
         mapping = aes(x = midPos, 
                       y = Fst, 
                       size = Nsites)) +
  geom_point(alpha = 0.75, color = "#869ca8") +
  scale_y_continuous(expand = c(0,0), 
                     limits = c(-0.05, 1)) +
  scale_size_continuous(range = c(0.5, 3)) +
  labs(x = "Position", 
       y = "Fst", 
       title = "N. Atlantic Anadromous vs Great Lakes Landlocked Alewife Chromosome 2", 
       subtitle = "Size 50,000 Step 10,000") +
  theme_bw() +
  theme(legend.position = "none",
        panel.grid.major.x = element_blank(),
        panel.grid.minor.x = element_blank(),
        axis.title.y = element_markdown(),
        axis.text.x = element_text(angle = 90,
                                  size = 8,
                                  vjust = 0.5))
nxg50_spike_plot

mxf10_plot <- ggplot(data = mxf10, 
                     mapping = aes(x = pos_cum, 
                                   y = Fst, 
                                   color = as_factor(chr))) +
  geom_point(alpha = 0.75, size = 0.5) +
  scale_x_continuous(label = mxf10_axis_set$chr, 
                     breaks = mxf10_axis_set$center) +
  scale_y_continuous(expand = c(0,0), 
                     limits = c(-0.05, 1)) +
  scale_color_manual(values = rep(c("#242b35", "#869ca8"), 
                                  unique(length(mxf10_axis_set$chr)))) +
  labs(x = NULL, 
       y = "Fst", 
       title = "Mid-Atlantic Anadromous vs Finger Lakes Landlocked Alewife", 
       subtitle = "Size 10,000 Step 2,000") +
  theme_bw() +
  theme(legend.position = "none",
        panel.grid.major.x = element_blank(),
        panel.grid.minor.x = element_blank(),
        axis.title.y = element_markdown(),
        axis.text.x = element_text(angle = 90,
                                  size = 8,
                                  vjust = 0.5))
mxf10_plot

mxf50_plot <- ggplot(data = mxf50, 
                     mapping = aes(x = pos_cum, 
                                   y = Fst, 
                                   color = as_factor(chr))) +
  geom_point(alpha = 0.75, size = 0.5) +
  scale_x_continuous(label = mxf50_axis_set$chr, 
                     breaks = mxf50_axis_set$center) +
  scale_y_continuous(expand = c(0,0), 
                     limits = c(-0.05, 1)) +
  scale_color_manual(values = rep(c("#242b35", "#869ca8"), 
                                  unique(length(mxf50_axis_set$chr)))) +
  labs(x = NULL, 
       y = "Fst", 
       title = "Mid-Atlantic Anadromous vs Finger Lakes Landlocked Alewife", 
       subtitle = "Size 50,000 Step 10,000") +
  theme_bw() +
  theme(legend.position = "none",
        panel.grid.major.x = element_blank(),
        panel.grid.minor.x = element_blank(),
        axis.title.y = element_markdown(),
        axis.text.x = element_text(angle = 90,
                                  size = 8,
                                  vjust = 0.5))
mxf50_plot

### Regions of Interest ###
## Looking at the same chromosomes for MIDA vs NATLA ##
mxf50_chr1_plot <- ggplot(data = filter(mxf50, chr == "NC_055957.1"), 
                     mapping = aes(x = pos_cum, 
                                   y = Fst)) +
  geom_point(alpha = 0.75, size = 0.5, color = "#242b35") +
  scale_x_continuous(label = mxf50_axis_set$chr, 
                     breaks = mxf50_axis_set$center) +
  scale_y_continuous(expand = c(0,0), 
                     limits = c(-0.05, 1)) +
  labs(x = NULL, 
       y = "Fst", 
       title = "Mid-Atlantic Anadromous vs Finger Lakes Landlocked Alewife", 
       subtitle = "Size 50,000 Step 10,000") +
  theme_bw() +
  theme(legend.position = "none",
        panel.grid.major.x = element_blank(),
        panel.grid.minor.x = element_blank(),
        axis.title.y = element_markdown(),
        axis.text.x = element_text(angle = 90,
                                  size = 8,
                                  vjust = 0.5))
mxf50_chr1_plot

mxf50_chr2_plot <- ggplot(data = filter(mxf50, chr == "NC_055958.1"), 
                     mapping = aes(x = pos_cum, 
                                   y = Fst)) +
  geom_point(alpha = 0.75, size = 0.5, color = "#869ca8") +
  scale_x_continuous(label = mxf50_axis_set$chr, 
                     breaks = mxf50_axis_set$center) +
  scale_y_continuous(expand = c(0,0), 
                     limits = c(-0.05, 1)) +
  labs(x = NULL, 
       y = "Fst", 
       title = "Mid-Atlantic Anadromous vs Finger Lakes Landlocked Alewife", 
       subtitle = "Size 50,000 Step 10,000") +
  theme_bw() +
  theme(legend.position = "none",
        panel.grid.major.x = element_blank(),
        panel.grid.minor.x = element_blank(),
        axis.title.y = element_markdown(),
        axis.text.x = element_text(angle = 90,
                                  size = 8,
                                  vjust = 0.5))
mxf50_chr2_plot

mxf50_chr3_plot <- ggplot(data = filter(mxf50, chr == "NC_055959.1"), 
                     mapping = aes(x = pos_cum, 
                                   y = Fst)) +
  geom_point(alpha = 0.75, size = 0.5, color = "#869ca8") +
  scale_x_continuous(label = mxf50_axis_set$chr, 
                     breaks = mxf50_axis_set$center) +
  scale_y_continuous(expand = c(0,0), 
                     limits = c(-0.05, 1)) +
  labs(x = NULL, 
       y = "Fst", 
       title = "Mid-Atlantic Anadromous vs Finger Lakes Landlocked Alewife", 
       subtitle = "Size 50,000 Step 10,000") +
  theme_bw() +
  theme(legend.position = "none",
        panel.grid.major.x = element_blank(),
        panel.grid.minor.x = element_blank(),
        axis.title.y = element_markdown(),
        axis.text.x = element_text(angle = 90,
                                  size = 8,
                                  vjust = 0.5))
mxf50_chr3_plot

mxf50_chr10_plot <- ggplot(data = filter(mxf50, chr == "NC_055966.1"), 
                     mapping = aes(x = pos_cum, 
                                   y = Fst)) +
  geom_point(alpha = 0.75, size = 0.5, color = "#242b35") +
  scale_x_continuous(label = mxf50_axis_set$chr, 
                     breaks = mxf50_axis_set$center) +
  scale_y_continuous(expand = c(0,0), 
                     limits = c(-0.05, 1)) +
  labs(x = NULL, 
       y = "Fst", 
       title = "Mid-Atlantic Anadromous vs Finger Lakes Landlocked Alewife", 
       subtitle = "Size 50,000 Step 10,000") +
  theme_bw() +
  theme(legend.position = "none",
        panel.grid.major.x = element_blank(),
        panel.grid.minor.x = element_blank(),
        axis.title.y = element_markdown(),
        axis.text.x = element_text(angle = 90,
                                  size = 8,
                                  vjust = 0.5))
mxf50_chr10_plot

mxf50_chr12_plot <- ggplot(data = filter(mxf50, chr == "NC_055968.1"), 
                     mapping = aes(x = pos_cum, 
                                   y = Fst)) +
  geom_point(alpha = 0.75, size = 0.5, color = "#242b35") +
  scale_x_continuous(label = mxf50_axis_set$chr, 
                     breaks = mxf50_axis_set$center) +
  scale_y_continuous(expand = c(0,0), 
                     limits = c(-0.05, 1)) +
  labs(x = NULL, 
       y = "Fst", 
       title = "Mid-Atlantic Anadromous vs Finger Lakes Landlocked Alewife", 
       subtitle = "Size 50,000 Step 10,000") +
  theme_bw() +
  theme(legend.position = "none",
        panel.grid.major.x = element_blank(),
        panel.grid.minor.x = element_blank(),
        axis.title.y = element_markdown(),
        axis.text.x = element_text(angle = 90,
                                  size = 8,
                                  vjust = 0.5))
mxf50_chr12_plot

### Chromosome 2 Spike Region ###

mxf50_spike_plot <- mxf50 %>%
  filter(chr == "NC_055958.1") %>%
  filter(midPos >= 16600000) %>%
  filter(midPos <= 17000000) %>%
  ggplot(.,
         mapping = aes(x = midPos, 
                       y = Fst, 
                       size = Nsites)) +
  geom_point(alpha = 0.75, color = "#869ca8") +
  scale_y_continuous(expand = c(0,0), 
                     limits = c(-0.05, 1)) +
  scale_size_continuous(range = c(0.5, 3)) +
  labs(x = "Position", 
       y = "Fst", 
       title = "Mid-Atlantic Anadromous vs Finger Lakes Landlocked Alewife Chromosome 2", 
       subtitle = "Size 50,000 Step 10,000") +
  theme_bw() +
  theme(legend.position = "none",
        panel.grid.major.x = element_blank(),
        panel.grid.minor.x = element_blank(),
        axis.title.y = element_markdown(),
        axis.text.x = element_text(angle = 90,
                                  size = 8,
                                  vjust = 0.5))
mxf50_spike_plot

nxf10_plot <- ggplot(data = nxf10, 
                     mapping = aes(x = pos_cum, 
                                   y = Fst, 
                                   color = as_factor(chr))) +
  geom_point(alpha = 0.75, size = 0.5) +
  scale_x_continuous(label = nxf10_axis_set$chr, 
                     breaks = nxf10_axis_set$center) +
  scale_y_continuous(expand = c(0,0), 
                     limits = c(-0.05, 1)) +
  scale_color_manual(values = rep(c("#242b35", "#869ca8"), 
                                  unique(length(nxf10_axis_set$chr)))) +
  labs(x = NULL, 
       y = "Fst", 
       title = "N. Atlantic Anadromous vs Finger Lakes Landlocked Alewife", 
       subtitle = "Size 10,000 Step 2,000") +
  theme_bw() +
  theme(legend.position = "none",
        panel.grid.major.x = element_blank(),
        panel.grid.minor.x = element_blank(),
        axis.title.y = element_markdown(),
        axis.text.x = element_text(angle = 90,
                                  size = 8,
                                  vjust = 0.5))
nxf10_plot

nxf50_plot <- ggplot(data = nxf50, 
                     mapping = aes(x = pos_cum, 
                                   y = Fst, 
                                   color = as_factor(chr))) +
  geom_point(alpha = 0.75, size = 0.5) +
  scale_x_continuous(label = nxf50_axis_set$chr, 
                     breaks = nxf50_axis_set$center) +
  scale_y_continuous(expand = c(0,0), 
                     limits = c(-0.05, 1)) +
  scale_color_manual(values = rep(c("#242b35", "#869ca8"), 
                                  unique(length(nxf50_axis_set$chr)))) +
  labs(x = NULL, 
       y = "Fst", 
       title = "N. Atlantic Anadromous vs Finger Lakes Landlocked Alewife", 
       subtitle = "Size 50,000 Step 10,000") +
  theme_bw() +
  theme(legend.position = "none",
        panel.grid.major.x = element_blank(),
        panel.grid.minor.x = element_blank(),
        axis.title.y = element_markdown(),
        axis.text.x = element_text(angle = 90,
                                  size = 8,
                                  vjust = 0.5))
nxf50_plot

### Regions of Interest ###
## Looking at the same chromosomes for MIDA vs NATLA ##
nxf50_chr1_plot <- ggplot(data = filter(nxf50, chr == "NC_055957.1"), 
                     mapping = aes(x = pos_cum, 
                                   y = Fst)) +
  geom_point(alpha = 0.75, size = 0.5, color = "#242b35") +
  scale_x_continuous(label = nxf50_axis_set$chr, 
                     breaks = nxf50_axis_set$center) +
  scale_y_continuous(expand = c(0,0), 
                     limits = c(-0.05, 1)) +
  labs(x = NULL, 
       y = "Fst", 
       title = "N. Atlantic Anadromous vs Finger Lakes Landlocked Alewife", 
       subtitle = "Size 50,000 Step 10,000") +
  theme_bw() +
  theme(legend.position = "none",
        panel.grid.major.x = element_blank(),
        panel.grid.minor.x = element_blank(),
        axis.title.y = element_markdown(),
        axis.text.x = element_text(angle = 90,
                                  size = 8,
                                  vjust = 0.5))
nxf50_chr1_plot

nxf50_chr2_plot <- ggplot(data = filter(nxf50, chr == "NC_055958.1"), 
                     mapping = aes(x = pos_cum, 
                                   y = Fst)) +
  geom_point(alpha = 0.75, size = 0.5, color = "#869ca8") +
  scale_x_continuous(label = nxf50_axis_set$chr, 
                     breaks = nxf50_axis_set$center) +
  scale_y_continuous(expand = c(0,0), 
                     limits = c(-0.05, 1)) +
  labs(x = NULL, 
       y = "Fst", 
       title = "N. Atlantic Anadromous vs Finger Lakes Landlocked Alewife", 
       subtitle = "Size 50,000 Step 10,000") +
  theme_bw() +
  theme(legend.position = "none",
        panel.grid.major.x = element_blank(),
        panel.grid.minor.x = element_blank(),
        axis.title.y = element_markdown(),
        axis.text.x = element_text(angle = 90,
                                  size = 8,
                                  vjust = 0.5))
nxf50_chr2_plot

nxf50_chr3_plot <- ggplot(data = filter(nxf50, chr == "NC_055959.1"), 
                     mapping = aes(x = pos_cum, 
                                   y = Fst)) +
  geom_point(alpha = 0.75, size = 0.5, color = "#869ca8") +
  scale_x_continuous(label = nxf50_axis_set$chr, 
                     breaks = nxf50_axis_set$center) +
  scale_y_continuous(expand = c(0,0), 
                     limits = c(-0.05, 1)) +
  labs(x = NULL, 
       y = "Fst", 
       title = "N. Atlantic Anadromous vs Finger Lakes Landlocked Alewife", 
       subtitle = "Size 50,000 Step 10,000") +
  theme_bw() +
  theme(legend.position = "none",
        panel.grid.major.x = element_blank(),
        panel.grid.minor.x = element_blank(),
        axis.title.y = element_markdown(),
        axis.text.x = element_text(angle = 90,
                                  size = 8,
                                  vjust = 0.5))
nxf50_chr3_plot

nxf50_chr10_plot <- ggplot(data = filter(nxf50, chr == "NC_055966.1"), 
                     mapping = aes(x = pos_cum, 
                                   y = Fst)) +
  geom_point(alpha = 0.75, size = 0.5, color = "#242b35") +
  scale_x_continuous(label = nxf50_axis_set$chr, 
                     breaks = nxf50_axis_set$center) +
  scale_y_continuous(expand = c(0,0), 
                     limits = c(-0.05, 1)) +
  labs(x = NULL, 
       y = "Fst", 
       title = "N. Atlantic Anadromous vs Finger Lakes Landlocked Alewife", 
       subtitle = "Size 50,000 Step 10,000") +
  theme_bw() +
  theme(legend.position = "none",
        panel.grid.major.x = element_blank(),
        panel.grid.minor.x = element_blank(),
        axis.title.y = element_markdown(),
        axis.text.x = element_text(angle = 90,
                                  size = 8,
                                  vjust = 0.5))
nxf50_chr10_plot

nxf50_chr12_plot <- ggplot(data = filter(nxf50, chr == "NC_055968.1"), 
                     mapping = aes(x = pos_cum, 
                                   y = Fst)) +
  geom_point(alpha = 0.75, size = 0.5, color = "#242b35") +
  scale_x_continuous(label = nxf50_axis_set$chr, 
                     breaks = nxf50_axis_set$center) +
  scale_y_continuous(expand = c(0,0), 
                     limits = c(-0.05, 1)) +
  labs(x = NULL, 
       y = "Fst", 
       title = "N. Atlantic Anadromous vs Finger Lakes Landlocked Alewife", 
       subtitle = "Size 50,000 Step 10,000") +
  theme_bw() +
  theme(legend.position = "none",
        panel.grid.major.x = element_blank(),
        panel.grid.minor.x = element_blank(),
        axis.title.y = element_markdown(),
        axis.text.x = element_text(angle = 90,
                                  size = 8,
                                  vjust = 0.5))
nxf50_chr12_plot

### Chromosome 2 Spike Region ###

nxf50_spike_plot <- nxf50 %>%
  filter(chr == "NC_055958.1") %>%
  filter(midPos >= 16600000) %>%
  filter(midPos <= 17000000) %>%
  ggplot(.,
         mapping = aes(x = midPos, 
                       y = Fst, 
                       size = Nsites)) +
  geom_point(alpha = 0.75, color = "#869ca8") +
  scale_y_continuous(expand = c(0,0), 
                     limits = c(-0.05, 1)) +
  scale_size_continuous(range = c(0.5, 3)) +
  labs(x = "Position", 
       y = "Fst", 
       title = "N. Atlantic Anadromous vs Finger Lakes Landlocked Alewife Chromosome 2", 
       subtitle = "Size 50,000 Step 10,000") +
  theme_bw() +
  theme(legend.position = "none",
        panel.grid.major.x = element_blank(),
        panel.grid.minor.x = element_blank(),
        axis.title.y = element_markdown(),
        axis.text.x = element_text(angle = 90,
                                  size = 8,
                                  vjust = 0.5))
nxf50_spike_plot

### Using ggsave to save the manhattan plots, or as I will now refer to it: ###
# Saving Private Plots (Ryan lol) ##
ggsave("figures/sliding-windows-fst/NATLA-x-GRTL-sz50-chrom2-spike.png", 
       plot = nxg50_chr2_spike_plot, 
       width = 10, 
       height = 4)

Error: object 'nxg50_chr2_spike_plot' not found